Receptor
PDB id Resolution Class Description Source Keywords
4D56 2.1 Å NON-ENZYME: OTHER UNDERSTANDING BI-SPECIFICITY OF A-DOMAINS PLANKTOTHRIX AGARDHII HYDROLASE NON-RIBOSOMAL PEPTIDE SYNTHETASE ADENYLATION A
Ref.: STRUCTURAL ELUCIDATION OF THE BISPECIFICITY OF A DO A BASIS FOR ACTIVATING NON-NATURAL AMINO ACIDS. ANGEW.CHEM.INT.ED.ENGL. V. 54 8833 2015
Ligand
Ligand Chain:Residue Validity Ligand Warnings Binding Data NGL Viewer Molecular Weight (Da) Formula SMILES
GOL A:1494;
Invalid;
none;
submit data
92.094 C3 H8 O3 C(C(C...
TYR AMP A:1491;
Valid;
none;
submit data
510.4 n/a [P+](...
PO4 A:1493;
A:1492;
Invalid;
Invalid;
none;
none;
submit data
94.971 O4 P [O-]P...
View in 3D viewer
90% Homology Family
Leader
PDB id Resolution Class Description Source Keywords
4D57 2 Å NON-ENZYME: OTHER UNDERSTANDING BI-SPECIFICITY OF A-DOMAINS PLANKTOTHRIX AGARDHII TRANSCRIPTION NON-RIBOSOMAL PEPTIDE SYNTHETASE ADENYLATIONDOMAIN
Ref.: STRUCTURAL ELUCIDATION OF THE BISPECIFICITY OF A DO A BASIS FOR ACTIVATING NON-NATURAL AMINO ACIDS. ANGEW.CHEM.INT.ED.ENGL. V. 54 8833 2015
Members (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1256 families.
1 4D4G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 4D56 - TYR AMP n/a n/a
3 4D57 - ARG AMP n/a n/a
4 4D4I - ARG C6 H15 N4 O2 C(C[C@@H](....
70% Homology Family (4)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 1068 families.
1 4D4G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 4D56 - TYR AMP n/a n/a
3 4D57 - ARG AMP n/a n/a
4 4D4I - ARG C6 H15 N4 O2 C(C[C@@H](....
50% Homology Family (5)
No: PDB id Binding Data Representative ligand Formula Smiles
The Class containing this family consists of a total of 922 families.
1 4D4G - ANP C10 H17 N6 O12 P3 c1nc(c2c(n....
2 4D56 - TYR AMP n/a n/a
3 4D57 - ARG AMP n/a n/a
4 4D4I - ARG C6 H15 N4 O2 C(C[C@@H](....
5 1AMU - AMP C10 H14 N5 O7 P c1nc(c2c(n....
Polypharmacology
Similar Ligands
Ligand no: 1; Ligand: TYR AMP; Similar ligands found: 258
No: Ligand ECFP6 Tc MDL keys Tc
1 TYR AMP 1 1
2 DAL AMP 0.744681 0.945946
3 ARG AMP 0.688679 0.865854
4 GAP 0.673684 0.933333
5 YAP 0.663462 0.96
6 ADP MG 0.621053 0.894737
7 ADP BEF 0.614583 0.871795
8 BEF ADP 0.614583 0.871795
9 MYR AMP 0.613208 0.853659
10 AMP MG 0.608696 0.881579
11 ADP PO3 0.602041 0.931507
12 ATP MG 0.59596 0.894737
13 ANP MG 0.588235 0.860759
14 CA0 0.587629 0.907895
15 AMP 0.586957 0.88
16 A 0.586957 0.88
17 5AL 0.584158 0.92
18 LPA AMP 0.578947 0.853659
19 ADP ALF 0.578431 0.860759
20 ALF ADP 0.578431 0.860759
21 A12 0.572917 0.848101
22 AP2 0.572917 0.848101
23 VO4 ADP 0.572816 0.894737
24 SRP 0.572816 0.921053
25 ADP VO4 0.572816 0.894737
26 FA5 0.572727 0.946667
27 ADP BMA 0.570093 0.933333
28 ABM 0.568421 0.857143
29 A2D 0.568421 0.906667
30 YSA 0.567568 0.813953
31 ADP 0.56701 0.881579
32 BA3 0.556701 0.906667
33 8QN 0.556604 0.92
34 PAJ 0.551402 0.851852
35 4AD 0.551402 0.934211
36 AMO 0.551402 0.921053
37 AP5 0.55102 0.906667
38 B4P 0.55102 0.906667
39 A A 0.550459 0.906667
40 AMP DBH 0.548673 0.933333
41 SRA 0.547368 0.835443
42 DLL 0.546296 0.945946
43 PTJ 0.545455 0.8625
44 ME8 0.545455 0.853659
45 AN2 0.545455 0.87013
46 SON 0.545455 0.896104
47 APC 0.544554 0.848101
48 LA8 ALF 3PG 0.542373 0.875
49 ALF ADP 3PG 0.542373 0.875
50 OOB 0.542056 0.945946
51 AU1 0.54 0.858974
52 M33 0.54 0.87013
53 ADX 0.54 0.797619
54 ADV 0.539216 0.871795
55 RBY 0.539216 0.871795
56 LAD 0.536364 0.875
57 WAQ 0.536364 0.873418
58 9SN 0.535714 0.886076
59 ATP 0.534653 0.881579
60 50T 0.534653 0.846154
61 ACP 0.534653 0.858974
62 00A 0.53211 0.897436
63 NB8 0.531532 0.886076
64 1ZZ 0.531532 0.831325
65 FYA 0.531532 0.894737
66 ATP A A A 0.530973 0.945205
67 AQP 0.529412 0.881579
68 APR 0.529412 0.906667
69 PRX 0.529412 0.835443
70 5FA 0.529412 0.881579
71 AF3 ADP 3PG 0.529412 0.875
72 AR6 0.529412 0.906667
73 3UK 0.527273 0.933333
74 AGS 0.524272 0.8375
75 AD9 0.524272 0.858974
76 SAP 0.524272 0.8375
77 AHX 0.518182 0.8625
78 TXA 0.517857 0.896104
79 AHZ 0.516949 0.853659
80 TYM 0.516667 0.946667
81 NAD IBO 0.516129 0.909091
82 AMP NAD 0.515385 0.946667
83 TAT 0.514286 0.848101
84 ANP 0.514286 0.858974
85 ACQ 0.514286 0.858974
86 PR8 0.508929 0.864198
87 ATF 0.504673 0.848101
88 A22 0.504587 0.894737
89 MAP 0.504587 0.8375
90 LAQ 0.504202 0.831325
91 YLB 0.5 0.833333
92 OAD 0.5 0.907895
93 NAD 0.5 0.945946
94 AR6 AR6 0.5 0.958904
95 7MD 0.5 0.853659
96 YLP 0.5 0.833333
97 25A 0.5 0.906667
98 ADQ 0.495495 0.907895
99 A1R 0.495495 0.85
100 AOC 0.494949 0.789474
101 ZID 0.492424 0.933333
102 A3D 0.492188 0.933333
103 JB6 0.491228 0.85
104 3OD 0.491228 0.907895
105 NVA LMS 0.491071 0.775281
106 D3Y 0.490909 0.828947
107 YLC 0.487805 0.853659
108 7MC 0.487805 0.833333
109 4UU 0.487395 0.909091
110 XAH 0.487179 0.831325
111 LEU LMS 0.486726 0.775281
112 5SV 0.486486 0.795181
113 NAQ 0.484848 0.886076
114 4UV 0.483051 0.909091
115 TSB 0.477477 0.770115
116 NAE 0.477273 0.909091
117 A5A 0.477064 0.77907
118 NAJ PZO 0.476923 0.886076
119 G5A 0.476636 0.772727
120 YLA 0.47619 0.833333
121 5X8 0.47619 0.802632
122 5AS 0.475728 0.733333
123 48N 0.47541 0.8625
124 25L 0.474138 0.894737
125 NAJ PYZ 0.473684 0.864198
126 5CD 0.473118 0.773333
127 SSA 0.472727 0.772727
128 RAB 0.472527 0.786667
129 ADN 0.472527 0.786667
130 XYA 0.472527 0.786667
131 AYB 0.472441 0.823529
132 4UW 0.471545 0.875
133 DND 0.471545 0.946667
134 NXX 0.471545 0.946667
135 NAI 0.471545 0.873418
136 TAD 0.471074 0.829268
137 NDE 0.471014 0.921053
138 M24 0.469697 0.864198
139 GSU 0.469565 0.793103
140 DTA 0.46875 0.779221
141 VMS 0.468468 0.761364
142 52H 0.468468 0.752809
143 54H 0.468468 0.761364
144 IOT 0.468254 0.823529
145 BIS 0.465517 0.82716
146 G A A A 0.465116 0.886076
147 4TA 0.465116 0.865854
148 5CA 0.464286 0.772727
149 53H 0.464286 0.752809
150 5N5 0.462366 0.763158
151 NAX 0.459677 0.864198
152 TXD 0.459677 0.873418
153 SMM 0.459459 0.741176
154 YLY 0.458647 0.823529
155 A4D 0.457447 0.763158
156 P5A 0.456897 0.73913
157 NSS 0.45614 0.793103
158 LSS 0.45614 0.755556
159 DSZ 0.45614 0.793103
160 OMR 0.456 0.821429
161 TXE 0.456 0.873418
162 3DH 0.454545 0.74359
163 NDC 0.453901 0.886076
164 COD 0.453846 0.784091
165 M2T 0.453608 0.728395
166 A3P 0.451923 0.88
167 AFH 0.45082 0.851852
168 BT5 0.450382 0.823529
169 U A G G 0.450382 0.897436
170 DZD 0.450382 0.851852
171 MTA 0.44898 0.74359
172 SFG 0.448598 0.789474
173 PO4 PO4 A A A A PO4 0.448276 0.917808
174 6V0 0.448 0.8625
175 SAM 0.445455 0.746988
176 Z5A 0.445255 0.835294
177 WSA 0.444444 0.802326
178 KAA 0.444444 0.747253
179 EP4 0.443299 0.725
180 G3A 0.442623 0.8625
181 EEM 0.441441 0.746988
182 6RE 0.441176 0.753086
183 AP0 0.440945 0.839506
184 PAP 0.440367 0.868421
185 G5P 0.439024 0.8625
186 CNA 0.438462 0.946667
187 A2P 0.438095 0.866667
188 N0B 0.437956 0.855422
189 SAH 0.436364 0.782051
190 A A A 0.435897 0.894737
191 3AM 0.435644 0.842105
192 GTA 0.435484 0.853659
193 N01 0.432836 0.945946
194 J7C 0.432692 0.740741
195 NAD BBN 0.432432 0.833333
196 NMN AMP PO4 0.431818 0.909091
197 ADJ 0.430769 0.843373
198 139 0.430769 0.864198
199 T5A 0.430769 0.833333
200 7D5 0.43 0.797468
201 S4M 0.428571 0.681818
202 6AD 0.428571 0.807229
203 ATR 0.427273 0.855263
204 A5D 0.427273 0.779221
205 SA8 0.427273 0.743902
206 NAD CJ3 0.426667 0.804598
207 A4P 0.426357 0.813953
208 A U 0.426357 0.909091
209 UP5 0.425197 0.884615
210 KB1 0.425 0.756098
211 4YB 0.424 0.795455
212 SAI 0.423423 0.772152
213 DSH 0.423077 0.719512
214 GEK 0.422414 0.797468
215 S7M 0.421053 0.746988
216 3NZ 0.420168 0.820513
217 7C5 0.419355 0.833333
218 IMO 0.419048 0.866667
219 A3N 0.419048 0.734177
220 UPA 0.418605 0.873418
221 4TC 0.418605 0.8625
222 2A5 0.418182 0.8125
223 ZAS 0.417476 0.782051
224 A7D 0.416667 0.746835
225 PPS 0.415929 0.776471
226 GJV 0.415094 0.743902
227 7D3 0.415094 0.8
228 NJP 0.413534 0.934211
229 NAD TDB 0.4125 0.68932
230 A6D 0.411765 0.738095
231 EAD 0.411348 0.864198
232 MAO 0.411215 0.732558
233 649 0.410853 0.777778
234 P1H 0.409722 0.843373
235 A3G 0.409524 0.792208
236 4CA 0.409396 0.788889
237 A3T 0.409091 0.789474
238 DAL FAD PER 0.407643 0.845238
239 NAP 0.407143 0.933333
240 V3L 0.40708 0.906667
241 0UM 0.40678 0.73494
242 A2R 0.405172 0.894737
243 5AD 0.404255 0.716216
244 A3S 0.40367 0.802632
245 AAT 0.403509 0.702381
246 62X 0.403361 0.701149
247 U G A 0.402685 0.853659
248 NAD NDT 0.402516 0.721649
249 U A C C 0.40146 0.897436
250 NA0 0.401408 0.921053
251 MHZ 0.4 0.674157
252 2SA 0.4 0.896104
253 BTX 0.4 0.811765
254 ITT 0.4 0.855263
255 AV2 0.4 0.810127
256 OVE 0.4 0.8
257 NHD 0.4 0.945946
258 7D4 0.4 0.8
Similar Binding Sites (Proteins are less than 50% similar to leader)
Pocket No.: 1; Query (leader) PDB : 4D57; Ligand: ARG AMP; Similar sites found: 44
This union binding pocket(no: 1) in the query (biounit: 4d57.bio1) has 37 residues
No: Leader PDB Ligand P-value (APoc) PS_Score (APoc) Sequence Similarity
1 3EXS 5RP 0.01283 0.42742 1.35747
2 3LTW HLZ 0.04392 0.40624 2.14286
3 2Y4O DLL 0.000000003926 0.54688 2.48307
4 4KBA 1QM 0.01393 0.42977 3.92749
5 4BG4 ARG 0.03312 0.41371 3.93258
6 2YPI PGA 0.02415 0.4132 4.04858
7 4OEV OXL 0.04443 0.4086 4.25101
8 3A6T 8OG 0.02392 0.40307 4.65116
9 1QD0 RR6 0.03603 0.40416 6.25
10 2X1L ADN 0.0406 0.40505 6.87023
11 2Y4N DLL 0.0000002196 0.51935 11.6705
12 2Y4N PAC 0.000001547 0.45886 11.6705
13 5MST FUM 0.00000004385 0.51435 25.4799
14 5MST AMP 0.000000006798 0.50223 25.4799
15 5MSD BEZ 0.000000002565 0.5283 28.0977
16 5MSD AMP 0.000000008425 0.49026 28.0977
17 5HM3 649 0.0000007796 0.54644 28.4468
18 5EY9 5SV 0.000001143 0.48271 28.9703
19 3KXW 1ZZ 0.00000002741 0.53597 32.1117
20 5D6J ATP 0.00002036 0.41753 32.2862
21 5OE4 3UK 0.00000001859 0.66218 36.3636
22 1PG4 COA 0.00000008662 0.5046 37.1728
23 1PG4 PRX 0.00000008662 0.5046 37.1728
24 3IES M24 0.00000005745 0.56051 38.657
25 1MDB AMP DBH 0.00000004727 0.49334 39.5176
26 2D1S SLU 0.00000001834 0.55872 39.5985
27 3C5E ATP 0.00000008794 0.58329 40.1754
28 4FUT ATP 0.0000006585 0.4572 40.7555
29 1V25 ANP 0.000000006789 0.60303 41.22
30 5BSR COA 0.000000007386 0.62804 41.6974
31 5BSR AMP 0.00000001557 0.59613 41.6974
32 4GXQ ATP 0.0000001724 0.47949 41.6996
33 4RLQ 3SK 0.0000003957 0.50754 42.0039
34 4DG8 AMP 0.0000000001409 0.52709 42.0593
35 3O84 HTJ 0.000002093 0.54912 42.4632
36 5X8G S0N 0.000000001884 0.6416 43.0928
37 3NYQ AMP 0.00000001062 0.5812 43.5644
38 3NYQ MCA 0.0000000127 0.57335 43.5644
39 3CW9 AMP 0.000000005216 0.71305 43.8492
40 3CW9 01A 0.0004919 0.44488 43.8492
41 4OXI GAP 0.00000000000008682 0.6494 44.2708
42 5IE3 OXD 0.000000254 0.51542 44.358
43 5IE3 AMP 0.000000254 0.51542 44.358
44 5C5H 4YB 0.00000004074 0.53236 45.4746
Feedback